Novel SERPINC1 variants in hereditary Antithrombin Deficiency: first pathogenic deep-intronic variant, revealed by multiple genomic and transcriptomic approaches

BACKGROUND: Antithrombin deficiency is a rare hereditary predisposition to venous thromboembolism caused by variants in the SERPINC1 gene. In up to 20% of cases, no explanatory variant is identified. OBJECTIVES: To uncover novel variants by covering the full SERPINC1 region. METHODS: In this single-centre cohort study, we included antithrombin deficient families in which no SERPINC1 variant had been previously identified. We used multiple genomic and transcriptomic approaches to identify novel variants and assess their pathogenicity. Variants were classified according to SERPINC1-specific ACMG criteria. RESULTS: We included ten families with 42 individuals and identified three novel SERPINC1 (NM_000488.4) variants: c.42-209T>G, c.1153+429C>T and c.916T>G. In addition, we identified an exon 6 deletion of uncertain novelty. All variants cosegregated perfectly. Despite being highly suspect, c.42-209T>G was the only variant of uncertain significance according to ACMG criteria, which prompted us to perform functional testing. Prediction tools suggested the introduction of an acceptor splice site at c.42-208, resulting in the inclusion of a pseudo-exon with premature stopcodon. We confirmed this aberrant splicing prediction by qPCR and Sanger sequencing of cDNA synthesised from RNA isolated from genomic edited HepG2 cells. c.42-209T>G leads to a reduction of SERPINC1 transcript levels. CONCLUSION: We report several novel SERPINC1 variants, one of which is the first pathogenic deep-intronic variant causing antithrombin deficiency through aberrant splicing. This finding improves our understanding of the genetic aetiology and clinical practice for antithrombin deficiency. In all tested families registered with our institution, an explanatory SERPINC1 variant has now been identified.